If we take the definition of atmosphere types literally, then yes it would count as two separate types.
However, I get what you're saying. And yeah, Chernobyl is a pretty good example. Also, active volcanoes tend to spew out some pretty nasty stuff.
The question is, is the area affected large enough to warrant a mention on a planetary survey? If you had to describe a world in 100 worlds or less, would you consider the affected area enough of a priority to include it in the report.
Now obviously when you're doing a submission, you have more than 100 words to work with, but the same principle applies. You're not writing a doctorate's thesis on the place, you're establishing the baseline for RP. If the problem is widespread enough that you think it would have a pronounced affect on an RP that would take place there, then by all means, bring it up.
Hope that helps.
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